Download or read book Photophysical Properties and Applications of Fluorescent Probes in Studying DNA Conformation and Dynamics written by Elana Maria Shepherd Stennett and published by . This book was released on 2015 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescence spectroscopy is a popular technique that has been particularly useful in probing biological systems, especially with the invention of single molecule fluorescence. For example, Förster resonance energy transfer (FRET) is one tool that has been helpful in probing distances and conformational changes in biomolecules. In this work, important properties necessary in the quantification of FRET were investigated while FRET was also applied to gain insight into the dynamics of biological molecules. In particular, dynamics of damaged DNA was investigated. While damages in DNA are known to affect DNA structure, what remains unclear is how the presence of a lesion, or multiple lesions, affects the flexibility of DNA, especially in relation to damage recognition by repair enzymes. DNA conformational dynamics was probed by combining FRET and fluorescence anisotropy along with biochemical assays. The focus of this work was to investigate the relationship between dynamics and enzymatic repair. In addition, to properly quantify fluorescence and FRET data, photophysical phenomena of fluorophores, such as blinking, needs to be understood. The triplet formation of the single molecule dye TAMRA and the photoisomerization yield of two different modifications of the single molecule cyanine dye Cy3 were examined spectroscopically to aid in accurate data interpretation. The combination of the biophysical and physiochemical studies illustrates how fluorescence spectroscopy can be used to answer biological questions.
Download or read book Fluorescent Analogs of Biomolecular Building Blocks written by Marcus Wilhelmsson and published by John Wiley & Sons. This book was released on 2016-04-04 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescent Analogs of Biomolecular Building Blocks focuses on the design of fluorescent probes for the four major families of macromolecular building blocks. Compiling the expertise of multiple authors, this book moves from introductory chapters to an exploration of the design, synthesis, and implementation of new fluorescent analogues of biomolecular building blocks, including examples of small-molecule fluorophores and sensors that are part of biomolecular assemblies.
Download or read book Design Synthesis and Translational Applications of Fluorescent DNA Repair Probes written by David Lawrence Wilson and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The process of DNA repair is critical to the viability of life on earth. However, our understanding of DNA repair is only as good as the tools we have to study it. While many of the traditional biochemical methods first pioneered in the 1960s and 1970s have yielded numerous important discoveries, they are often laborious and indirect. Efforts to study the biology and therapeutic relevance of DNA repair pathways can be limited by such method, and novel tools are required to keep up with the expanding capabilities of other fields. Significant advances in optics, microprocessors, electrical engineering, and nanofabrication have led to the widespread use of fluorescent microplate readers, fluorescence microscopes and flow cytometry instruments. However, such advances are meaningless without fluorescent assays that are compatible with such instruments. In addition to their compatibility with powerful new technologies, fluorescent probes offer the advantage of being able to directly assay for DNA repair activity in a simple, mix-andmeasure format. This work describes several efforts to design, synthesize and apply fluorescent probes of DNA repair. Chapter 1 summarizes the distinct classes of probe designs and their potential utility in varied research and preclinical settings. This work has been adapted in part with permission from: Wilson, D. L.; Kool, E. T. ACS Chem. Biol. 2018, 13 (7), 1721--1733. Copyright 2018 American Chemical Society. Chapter 2 presents work on a real-time probe of the DNA demethylase ALKBH2. The DNA repair enzyme ALKBH2 is implicated in both tumorigenesis as well as resistance to chemotherapy in certain cancers. It is currently under study as a potential diagnostic marker and has been proposed as a therapeutic target. To date, however, there exist no direct methods for measuring the repair activity of ALKBH2 in vitro or in biological samples. In this chapter, we report a highly specific, fluorogenic probe design based on an oligonucleotide scaffold that reports directly on ALKBH2 activity both in vitro and in cell lysates. Importantly, the probe enables the monitoring of cellular regulation of ALKBH2 activity in response to treatment with the chemotherapy drug temozolomide through a simple fluorescence assay, which has only previously been observed through indirect means such as qPCR and western blots. Furthermore, the probe provides a viable high- Index vi throughput assay for drug discovery. This work has been adapted in part with permission from: Wilson, D. L.; Beharry, A. A.; Srivastava, A.; O'Connor, T. R.; Kool, E. T. Angew. Chem. Int. Ed. 2018, 57 (39), 12896--12900. Copyright 2018 Wiley-VCH. Chapter 3 describes the design and synthesis of probes to be used a general DNA glycosylase sensing platform. DNA glycosylases constitute a biologically and biomedically important group of DNA repair enzymes responsible for initiating base excision repair (BER). Measuring their activities can be useful for studying the mechanisms DNA damage and repair and for practical applications in cancer diagnosis and drug screening. Previous fluorescence methods for assaying DNA glycosylases are often complex and/or limited in scope to a single enzyme type. In this chapter we describe a universal base excision reporter (UBER) fluorescence probe design that implements an unprecedentedly rapid oxime reaction (> 150 M--1 s --1 ) with high specificity for the abasic (AP) site of DNA. The molecular rotor design achieves a robust > 250--500-fold increase in fluorescence upon reaction with AP sites in DNA. By using the fluorescence reporter in concert with specific DNA lesion-containing substrates, the UBER probe can be used in a coupled assay in principle with any DNA glycosylase. We demonstrate the utility of the UBER probe by assaying five different glycosylases in real time as well as profiling glycosylase activity in cell lysates. This work has been adapted in part with permission from: Wilson, D. L.; Kool, E. T. J. Am. Chem. Soc. 2019, 141 (49), 19379--19388. Copyright 2019 American Chemical Society. Chapter 4 explores preliminary data on a broad range of downstream applications for the UBER probe system outside of sensing DNA glycosylase activity including activator/inhibitor screening, AP site sensing in live cells, and nucleic acid sensing. Additionally we propose several other applications to exploit the unique chemical and photophysical properties of the UBER probes described in chapter 3.
Download or read book Studying the Solution Behavior of DNA and DNA Sliding Clamps Using Various Fluorescence Techniques written by Suman Ranjit and published by . This book was released on 2013 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
Download or read book Fluorescent Energy Transfer Nucleic Acid Probes written by Vladimir V. Didenko and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescent nucleic acid probes, which use energy transfer, include such constructs as molecular beacons, molecular break lights, Scorpion primers, TaqMan probes, and others. These probes signal detection of their targets by changing either the intensity or the color of their fluorescence. Not surpr- ingly, these luminous, multicolored probes carry more flashy names than their counterparts in the other fields of molecular biology. In recent years, fluor- cent probes and assays, which make use of energy transfer, have multiplied at a high rate and have found numerous applications. However, in spite of this explosive growth in the field, there are no manuals summarizing different p- tocols and fluorescent probe designs. In view of this, the main objective of Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols is to provide such a collection. Oligonucleotides with one or several chromophore tags can form fluor- cent probes capable of energy transfer. Energy transport within the probe can occur via the resonance energy transfer mechanism, also called Förster tra- fer, or by non-Förster transfer mechanisms. Although the probes using Förster transfer were developed and used first, the later non-Förster-based probes, such as molecular beacons, now represent an attractive and widely used option. The term “fluorescent energy transfer probes” in the title of this book covers both Förster-based fluorescence resonance energy transfer (FRET) probes and probes using non-FRET mechanisms. Energy transfer probes serve as molecule-size sensors, changing their fluorescence upon detection of various DNA reactions.
Download or read book Fluorescent Probes written by Godfrey S. Beddard and published by . This book was released on 1981 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: The photophysical and photochemical properties of probes in biological and in model systems are topics of intense current research. The wavelength, intensity, time and polarisation dependence of fluorescence probes can provide information on properties as diverse as electric fields and changes in conformation and may be used in the formidable task of establishing structure-function relationships in proteins and cell membranes. The wide scope of interactions which can be studied by these fluorescent molecules is illustrated in the articles in this volume which are based on talks, although much extended and updated, given at a meeting on 'Fluorescence Probes in Proteins and Membranes' held in the Royal Institution in November 1979.
Download or read book Fluorescent Probes to Investigate Homologous Recombination Dynamics written by Eric Parker Davenport and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: There are multiple mechanisms by which DNA can become damaged. Such damage must be repaired for the cell to avoid ill-health consequences. Homologous recombination (HR) is a means of repairing one specific type of damage, a double-strand break (DSB). This complex pathway includes the Rad51-DNA nucleoprotein filament as its primary machinery. Current methodology for studying HR proteins includes the use of fluorescently labeled DNA to probe for HR dynamics. This technique limits the number of proteins that can be involved in experimentation, and often only works as an end reporter. The work here aims at improving upon standard techniques by creating two fluorescent protein probes. The first probe was developed by directly attaching a fluorophore to Saccharomyces cerevisiae Rad51 with the use of click chemistry and the incorporation of unnatural amino acids. This probe could function as a primary reporter on the formation and dissociation of the Rad51-DNA filament in the presence of pro- and anti- HR mediator proteins. The second probe was created by labeling the exterior cysteine residues of Plasmodium falciparum single strand DNA binding protein (SSB) with a fluorophore via maleimide chemistry. This probe acts as a secondary reporter for HR dynamics by signaling for when free single stranded DNA (ssDNA) is available.
Download or read book Palladium Catalyzed Modification of Nucleosides Nucleotides and Oligonucleotides written by Anant R. Kapdi and published by Elsevier. This book was released on 2018-06-04 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Palladium-Catalyzed Modification of Nucleosides, Nucleotides and Oligonucleotides describes the procedures and protocols related to the modification of nucleosides, nucleotides and oligonucleotides via Pd-mediated cross-coupling processes. The book highlights the growing area of nucleic acid modification and how Pd-mediated coupling reactions can assist this development. Users will find key synthetic protocols for these reactions in this latest volume in the Latest Trends in Palladium Chemistry series. As most of the research in the field of antiviral agents has centered on the use of modified nucleosides that have exhibited promising activity, this book provides an up-to-date reference for both professionals in industry and other interested parties. - Provides synthetic routes for useful nucleoside molecules, information otherwise found only through time-consuming literature searches - Covers metal-mediated and metal-catalyzed cross coupling processes of nucleosides and related compounds - Includes Suzuki-Miyaura, Stille and Sonogashira reactions, as well as C-H bond functionalization - Highlights the growing area of nucleic acid modification and how Pd-mediated coupling reactions can assist
Download or read book Theoretical Studies of Dye labeled DNA Systems with Applications to Fluorescence Resonance Energy Transfer written by Elena Dolghih and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In this work we describe a molecular dynamics study of several dye-DNA systems in which we examine how fluorescent probes interact with DNA and the effects of these interactions on FRET. Structural fluctuations in interchromophore distances and dipole orientations of the probes, as well as rates and efficiencies of energy transfer are evaluated carefully in the light of Förster-proposed approximations. Theoretical results are compared to available experimental data and possible improvements in system design with respect to the location and the mode of attachment of the probes are proposed.
Download or read book Nucleic Acids written by Victor A. Bloomfield and published by Sterling Publishing Company. This book was released on 2000-04-17 with total page 854 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.
Download or read book Introduction to Fluorescence Sensing written by Alexander P. Demchenko and published by Springer Nature. This book was released on 2020-12-01 with total page 673 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides systematic knowledge of basic principles in the design of fluorescence sensing and imaging techniques together with critical analysis of recent developments. Fluorescence is the most popular technique in chemical and biological sensing because of its ultimate sensitivity, high temporal and spatial resolution and versatility that enables imaging within the living cells. It develops rapidly in the directions of constructing new molecular recognition units, new fluorescence reporters and in improving sensitivity of response up to detection of single molecules. Its application areas range from control of industrial processes to environment monitoring and clinical diagnostics. Being a guide for students and young researchers, it also addresses professionals involved in active basic and applied research. Making a strong link between education, research and product development, this book discusses prospects for future progress.
Download or read book DNA Technology written by Joseph R. Lakowicz and published by Springer. This book was released on 2013-04-25 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: During the past 15 years, there has been remarkable progress in the analysis and manipulation of DNA and its use in nanotechnology. DNA analysis is ubiquitous in molecular biology, medical diagnostics, and forensics. Much of the readout technology is based on fluorescence detection. This volume contains contributions from many experts in the field who present an overview of many aspects of DNA technology. These chapters provide an understanding of the underlying principles and technology, rather than an exhaustive review of the literature. Written in a clear straightforward style, this book is an excellent introduction for any scientist to the use of fluorescence in DNA analysis. DNA Technology is an essential reading for all academics, bench scientists, and industry professionals wishing to take advantage of the latest and greatest in this continuously emerging field. Key Features: *Comprehensive overview of the complexities of DNA analysis, *Covers topics of universal interest to a broad field of scientists, *Accessible utility in presenting state-of-the-art DNA technology, *Chapters authored by key figures in the field.
Download or read book Spectroscopy and Dynamics of Single Molecules written by and published by Elsevier. This book was released on 2019-08-14 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: Spectroscopy and Dynamics of Single Molecules: Methods and Applications reviews the most recent developments in spectroscopic methods and applications. Spectroscopic techniques are the chief experimental methods for testing theoretical models and research in this area plays an important role in stimulating new theoretical developments in physical chemistry. This book provides an authoritative insight into the latest advances in the field, highlighting new techniques, current applications, and potential future developments An ideal reference for chemists and physicists alike, Spectroscopy and Dynamics of Single Molecules: Methods and Applications is a useful guide for all those working in the research, design, or application of spectroscopic tools and techniques across a wide range of fields. - Includes the latest research on ultrafast vibrational and electronic dynamics, nonlinear spectroscopies, and single-molecule methods - Makes the content accessible to researchers in chemistry, biophysics, and chemical physics through a rigorous multi-disciplinary approach - Provides content edited by a world-renowned chemist with more than 30 years of experience in research and instruction
Download or read book Research Grants Index written by National Institutes of Health (U.S.). Division of Research Grants and published by . This book was released on 1975 with total page 1224 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Multi scale Quantum Models for Biocatalysis written by Darrin M. York and published by Springer Science & Business Media. This book was released on 2009-05-30 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: “Multi-scale Quantum Models for Biocatalysis” explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes. This book is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology and for students exposed to these research areas.
Download or read book New Trends in Fluorescence Spectroscopy written by Bernard Valeur and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: This first volume in the new Springer Series on Fluorescence brings together fundamental and applied research from this highly interdisciplinary and field, ranging from chemistry and physics to biology and medicine. Special attention is given to supramolecular systems, sensor applications, confocal microscopy and protein-protein interactions. This carefully edited collection of articles is an invaluable tool for practitioners and novices.
Download or read book Research Awards Index written by and published by . This book was released on 1977 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
